[MMTK] problems with molecular dynamics

michael.l.stoppelman.1 stoppeml@purdue.edu
Fri, 8 Nov 2002 12:06:38 -0500 (EST)


Here is the gdb output (Same sigsegv for Steep & Conjugate):

Program received signal SIGSEGV, Segmentation fault.
0xfeeada34 in ?? ()
   from
/home/champion/l/cbaileyk/cs590b/lib/python2.1/site-packages/MMTK/sunos5/MMTK_forcefield.so
(gdb) where
#0  0xfeeada34 in ?? ()
   from
/home/champion/l/cbaileyk/cs590b/lib/python2.1/site-packages/MMTK/sunos5/MMTK_forcefield.so
#1  0xfeead948 in ?? ()
   from
/home/champion/l/cbaileyk/cs590b/lib/python2.1/site-packages/MMTK/sunos5/MMTK_forcefield.so
#2  0xfeeae130 in ?? ()
   from
/home/champion/l/cbaileyk/cs590b/lib/python2.1/site-packages/MMTK/sunos5/MMTK_forcefield.so
#3  0xfeea656c in ?? ()
   from
/home/champion/l/cbaileyk/cs590b/lib/python2.1/site-packages/MMTK/sunos5/MMTK_forcefield.so
#4  0xfef10f4c in ?? ()
   from
/home/champion/l/cbaileyk/cs590b/lib/python2.1/site-packages/MMTK/sunos5/MMTK_minimization.so
#5  0x22d4c in PyEval_CallObjectWithKeywords ()
#6  0x22bdc in PyEval_CallObjectWithKeywords ()
#7  0x22a18 in PyEval_CallObjectWithKeywords ()
#8  0x72e2c in _PyUnicode_IsAlpha ()
#9  0x22d4c in PyEval_CallObjectWithKeywords ()
#10 0x22bdc in PyEval_CallObjectWithKeywords ()
#11 0x234e0 in PyEval_CallObjectWithKeywords ()
#12 0x20d0c in PyEval_EvalCode ()
---Type <return> to continue, or q <return> to quit---
#13 0x23078 in PyEval_CallObjectWithKeywords ()
#14 0x22bbc in PyEval_CallObjectWithKeywords ()
#15 0x22f24 in PyEval_CallObjectWithKeywords ()
#16 0x22b98 in PyEval_CallObjectWithKeywords ()
#17 0x22dbc in PyEval_CallObjectWithKeywords ()
#18 0x22c1c in PyEval_CallObjectWithKeywords ()
#19 0x234e0 in PyEval_CallObjectWithKeywords ()
#20 0x20de0 in PyEval_EvalCode ()
#21 0x1d330 in PyEval_EvalCode ()
#22 0x3a640 in PyRun_FileExFlags ()
#23 0x3a5ec in PyRun_FileExFlags ()
#24 0x3a5bc in PyRun_FileExFlags ()
#25 0x39800 in PyRun_SimpleFileExFlags ()
#26 0x39288 in PyRun_AnyFileExFlags ()
#27 0x19a24 in Py_Main ()
#28 0x19430 in main ()

------------------------------------------------ end of gdb


Now the weird this is I did try this code:

from MMTK.Minimization import SteepestDescentMinimizer
from MMTK import *
from MMTK.ForceFields import Amber94ForceField
from MMTK.Proteins import Protein


universe = InfiniteUniverse(Amber94ForceField())
universe.protein = Protein('insulin')
minimizer = SteepestDescentMinimizer(universe)
minimizer(steps = 100)


And it worked.

Can you tell me what versions of all things relevent to MMTK you're using
Conrad? Cause I think versions are important, cause that solved my
previous core dump.

-Mike



On 8 Nov 2002, Konrad Hinsen wrote:

> "michael.l.stoppelman.1" <stoppeml@purdue.edu> writes:
>
> > My first idea is to extend the PeptideChain class adding a addResidue
> > method.  After every addition to the PeptideChain I want to minimize the
> > energy over that chain. I attempted to do this with only two residues and
>
> Sounds like a good approach.
>
> > But first, I wanted to see if any of this would even work:
> ...
>
> > that code core dumps.
>
> It works fine on my system. There is certainly nothing wrong with your
> code, in fact, you should never get a core dump unless you write your
> own C code. In practice, you can crash Python in rare cases by using
> too much memory, but that's all I am aware of. I don't know of any bug
> in MMTK that would cause core dumps, although of course I certainly
> don't know all bugs!
>
> This seems to be a machine-specific problem, so I can't do much
> directly. Can you check with a debugger where the code is crashing? If
> it is in the minimizer, could you try a simple energy evaluation first
> to see if that works fine? And try the conjugate gradient minimizer
> for comparison?
>
> Konrad.
> --
> -------------------------------------------------------------------------------
> Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
> Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
> Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
> 45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
> France                                   | Nederlands/Francais
> -------------------------------------------------------------------------------
>
> _______________________________________________
> mmtk maillist  -  mmtk@starship.python.net
> http://starship.python.net/mailman/listinfo/mmtk
>